comparison tradis_gene_insert_sites.xml @ 1:58234d95978d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"

0:738e58ed9cc2

<tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@VERSION@">
    <description></description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        ]]>
    </command>
    
    <inputs>
        <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
        <param name="input_annot" type="data" format="txt" label="EMBL file containing the reference genome annotations"/>
       <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       
    </inputs>
    
    <outputs>
        <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv"/>
    </outputs>
    
    <tests>
        <test>
            <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
            <param name="input_annot" ftype="txt" value="tiny_ref.embl"/>
            <param name="trim3" ftype="float" value="0"/>
            <param name="trim5" ftype="float" value="0"/>
            <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.csv"  compare="sim_size" delta="200" />
        </test>
    </tests>

 </tool>

1:58234d95978d

<tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@TOOL_VERSION@+galaxy@VERSION@">
    <description></description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        ]]>
    </command>
    
    <inputs>
        <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
        <param name="input_annot" type="data" format="embl" label="EMBL file containing the reference genome annotations"/>
       <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       
    </inputs>
    
    <outputs>
        <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv" label="${tool.name} on ${on_string}"/>
    </outputs>
    
    <tests>
        <test>
            <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
            <param name="input_annot" ftype="embl" value="tiny_ref.embl"/>
            <param name="trim3" ftype="float" value="0"/>
            <param name="trim5" ftype="float" value="0"/>
            <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.csv"  compare="sim_size" delta="200" />
        </test>
    </tests>

 </tool>